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The main objective of the game is to get to the exit of each level, while destroying enemies and collecting points. Many objects onscreen can be shot including boxes, obstacles and blocks. Besides points, some collectibles include health powerups, gun powerups, and some inventory items with special abilities. The final level of each episode has no exit, and is instead completed by finding and defeating Dr. Proton.

At the end of every level (with the exception of the last level in each episode), the player can receive up to seven 10,000 point bonuses, earned by making certain achievements in the level, such as destroying all cameras. At least two other Apogee titles, Duke Nukem II and Rise of the Triad, have similar end-of-level bonuses.

The game is set in the year 1997 (which was the "near future" at the time of game release). Dr. Proton is a madman, determined to take over the world with his army of Techbots. Duke Nukem, the eponymous hero, takes upon the task of stopping him. The first episode takes place in the devastated city of Los Angeles. In the second episode, Duke chases Dr. Proton to his secret moonbase. In the third episode, Dr. Proton escapes into the future, and Duke pursues him through time, to put a permanent end to his mad schemes.

Due to technical limitations the game world scrolls by shifting 8x8 "blocks" rather than individual pixels. Similar techniques are used in e.g. Zeliard, Cosmo's Cosmic Adventure and Duke Nukem II. Console and arcade platform games would typically perform this using dedicated hardware, such as the PPU in the NES which can scroll the background.

After the game's release, Apogee Software became aware that the Captain Planet and the Planeteers animated series featured a character with the same name (Duke Nukem) and therefore to avoid a lawsuit, the software house renamed the 2.0 version of its game Duke Nukum.[5] It later turned out that Duke Nukem was not a registered name, so Apogee registered it and used the original Duke Nukem name in the sequels.[5][5]

Duke Nukem was followed by Duke Nukem II in 1993, featuring the same hero still without the dark sunglasses, and later Duke Nukem 3D in 1996. A third sequel, Duke Nukem Forever, was announced in 1997. Plagued by various developmental problems and delays, the game would later be picked up by Gearbox Software and released in 2011, fourteen years after the game was announced and twenty years after the first game was released. In a downloadable content (DLC) for that game, titled "The Doctor Who Cloned Me", Dr. Proton made his return.